Package index
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allocateCells() - Annotate all cells with contour level of cell type-specific density.
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cellsInRegion() - Check which cells are in which regions
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computeDensity() - Perform kernel density estimation on SpatialExperiment
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computeDensityHex() - Perform kernel density estimation on SpatialExperiment
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contour2sf() - Draw a contour region on some density level
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coord_hash() - Hash two 15-bytes signed integers into one 32-bytes integer.
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corDensity() - Test for density correlation between two cell types.
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findNbrsGrid() - Construct a neighbour list from grid coordinates.
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findNbrsSNN() - Construct a SNN neighbour list from assay.
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findNbrsSpatial() - Construct a distance-based neighbour list from cell coordinates.
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findROI() - Find ROIs based on cell type-specific densities via graph-based method.
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getClusters() - Cluster cells in spe using graph methods.
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getContour() - Get contour from density
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getContourRegions() - Calculate areas between every two density levels
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getNiche() - Build a niche assay based on the profile of neighbouring cells
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globalMoran() - Calculate global Moran for 1 to 2 variables.
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grid2df() - Convert x,y nodes to data.frame of polygons
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grid2sf() - Convert x,y nodes to sf polygons
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gridDensity() - Perform kernel density estimation on SpatialExperiment for cell types of interest
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gridSPE() - Summarize a SpatialExperiment object at grid-level
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localMoran() - Calculate local Moran for 1 to 2 variables.
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mergeROI() - Manually merge ROIs
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normalizeAssay() - Perform log normalization for counts
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plotCellCompo() - Plot cell type composition in each density level of cell of interest.
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plotContour() - Plot contour lines.
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plotContourRegion() - Visualising an sf object (for internal use only at the moment)
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plotCorHeatmap() - Plot model statistics using heatmap.
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plotDR()plotUMAP()plotPCA() - Plot reduced dimensions.
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plotDensCor() - Plot density correlation between two cell types
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plotDensity() - Plot grid-based density.
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plotGrid() - Plot grid from metadata.
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plotImage() - Plot background image of spe
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plotLISA() - Plotting LISA (e.g. moran)
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plotROI() - Plot ROIs on spatial.
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plotSpatial() - Plot cells based on spatial coordinates.
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postSelRegion() - Merge sel_region from the selectRegion function to SpatialExperiment.
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realignVisium() - Scale and straighten out Visium coordinates
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realignVisiumHD() - Scale and straighten out VisiumHD coordinates
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runPCA() - Fast PCA using irlba.
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runUMAP() - UMAP using uwot. Parameters are set to be similar to Seurat's
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selectRegion() - Select region of interest from plot
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spe2PB() - Given a 'SpatialExperiment' data object, create pseudo-bulk samples using the colData information and return a DGEList object
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`[`(<SpatialExperiment>,<ANY>,<ANY>,<ANY>) - Subset for grid level analysis
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update_bound() - Update the x,y limits of a plot